I imagine they wouldn't enter the roleplay at the beginning. An undercover character would enter earlier, but a more powerful antagonist would enter much later on, and be a full-on adult. I want the bad guys to be Team Rocket, and for them to somehow be connected with the legendaries originally turning on humans, but I didn't form any true details because I want that to be open for suggestion/character-driven. 

So, I guess the only real limit is when they will be introduced. We won't be fighting Elite Four level bosses at the beginning of the roleplay, after all. But, you could totally make an undercover character, a Giovanni-like character (cause Giovanni died of old age), or like an evil gym leader or elite four member. It's up to you.